Elena Formoso

Magnetic Endohedral Transition-Metal-Doped Semiconduncting-Nanoclusters

Endohedral first-row transition-metal-doped TM@Zn(i)S(i) nanoclusters, in which TM stands for the first-row transition-metals from Sc to Zn, and i=12, 16, have been characterized. In these structures the dopant metals are trapped inside spheroidal hollow semiconducting nanoclusters. It is observed that some of the transition metals are trapped in the center of mass of the cluster, whereas others are found to be displaced from that center, leading to structures in which the transition metals display a complex dynamical behavior upon encapsulation. This fact was confirmed by quantum molecular dynamics calculations, which further confirmed the thermal stability of endohedral compounds. In the endohedrally-doped nanoclusters in which the transition-metal atom sits on the center of mass, the host hollow cluster structure remains undistorted after dopant encapsulation. Conversely, if the encapsulated transition-metal atom is displaced from the center of mass, the host hollow cluster structure suffers a very tiny distortion. Additionally, it is found that there is negligible charge transfer between the dopant transition-metal atom and its hollow cluster host and, after encapsulation, the spin densities remain localized on the transition-metal atom. This allows for the atomic-like behavior of the trapped transition-metal atom, which gives rise to their atomic-like magnetic properties. The encapsulation free energies are negative, suggesting that these compounds are thermodynamically stable.

Aluminum interaction with 2,3-diphosphoglyceric acid. A computational study

The interaction of aluminum with 2,3-diphosphoglyceric acid (2,3-DPG) is thought to be one of the strongest interactions of aluminium with a biophosphate molecule. In this article, the affinity energies for a family of Al–(2,3-DPG) complexes are calculated at the DFT level of theory. The study includes a total of 26 structures that vary from 1 : 1 complexes, to 1 : 2 stoichiometry and ternary complexes with citrate, considering different coordination modes and protonation states. Our results demonstrate that in the case of 1 : 1 complexes, the 2,3-DPG ligand could compete with citrate for complexation with aluminum at physiological pH. However, for the rest of the complexes there is a clear preference for Al(Citr)2 > Al(2,3-DPG)(Citr) ternary complex > Al(2,3-DPG)2 complexes. For each of these groups the charge of the ligand determines the affinity but to a lower extent than the nature of the Citr/2,3-DPG ligands. In summary, our results point to a high variety of possible complexation modes of 2,3-DPG to aluminum, showing a higher preference towards the formation of ternary complexes.

Aluminum and its effect in the equilibrium between folded/unfolded conformation of NADH.

Nicotinamide adenine dinucleotide (NADH) is one of the most abundant cofactor employed by proteins and enzymes. The molecule is formed by two nucleotides that can lead to two main conformations: folded/closed and unfolded/open. Experimentally, it has been determined that the closed form is about 2 kcal/mol more stable than the open formed. Computationally, a correct description of the NADH unfolding process is challenging due to different reasons: 1) The unfolding process shows a very low energy difference between the two conformations 2) The molecule can form a high number of internal hydrogen bond interactions 3) Subtle effects such as dispersion may be important. In order to tackle all these effects, we have employed a number of different state of the art computational techniques, including: a) well-tempered metadynamics, b) geometry optimizations, and c) Quantum Theory of Atoms in Molecules (QTAIM) calculations, to investigate the conformational change of NADH in solution and interacting with aluminum. All the results indicate that aluminum indeed favors the closed conformation of NADH, due mainly to the formation of a more rigid structure through key hydrogen bond interactions.

A computational study on interaction of aluminum with D-glucose 6-phosphate for various stoichiometries

The interaction of aluminum with glucose 6-phosphate (Al-G6P) is thought to disrupt key processes of the glucide metabolism in cells. In this article, a Density Functional Theory study on the interaction of aluminum with D-glucose 6-phoshate is presented, combined with polarizable continuum models to account for bulk solvent effects. 143 aluminum–G6P complexes with different binding modes and various total charges are characterized comprising mononuclear (1 : 1, 1 : 2, 1 : 3, 1 : 1 : 1 (with citrate)) and dinuclear (2 : 1, 2 : 2) species. This large Al-G6P interaction dataset, the largest theoretical characterization of an aluminum–biophosphate interaction, gives insight into the diversity and complex picture of the interaction of aluminum with phosphate metabolites. We have found that charge and binding mode are driving factors in the binding affinity of glucose 6-phosphate. In addition, our calculations points to a tendency to form dicoordinated binding motifs, in which aluminum is bound to two functional groups of glucose 6-phosphate ligand. This tendency gives rise to a capacity of aluminum to act as a bridging agent in the coordination of several metabolites, a behavior that can be linked to the suspected tendency of aluminum to form aggregates that could induce various toxic effects in biological systems.

Aluminum's preferential binding site in proteins: Sidechain of amino acids versus backbone interactions

Abstract The interaction of aluminum ion Al(III) with polypeptides is a subject of paramount importance, since it is a central feature to understand its deleterious effects in biological systems. Various drastic effects have been attributed to aluminum in its interaction with polypeptides and proteins. These interactions are thought to be established mainly through the binding of aluminum to phosphorylated and non-phosphorylated amino acid sidechains. However, a new structural paradigm has recently been proposed, in which aluminum interacts directly with the backbone of the proteins, provoking drastic changes in their secondary structure and leading ultimately to their denaturation. In the present paper, we use computational methods to discuss the possibility of aluminum to interact with the backbone of peptides and compare it with the known ability of aluminum to interact with amino acid sidechains. To do so, we compare the thermodynamics of formation of prototype aluminum-backbone structures with prototype aluminum-sidechain structures, and compare these results with previous data generated in our group in which aluminum interacts with various types of polypeptides and known aluminum biochelators. Our results clearly points to a preference of aluminum towards amino acid sidechains, rather than towards the peptide backbone. Thus, structures in which aluminum is interacting with the carbonyl group are only slightly exothermic, and they become even less favorable if the interaction implies additionally the peptide nitrogen. However, structures in which aluminum is interacting with negatively-charged sidechains like aspartic acid, or phosphorylated serines are highly favored thermodynamically.

Structural and optical properties of the naked and passivated Al5Au5 bimetallic nanoclusters

The structural and optical properties of both the naked and passivated bimetallic Al5Au5 nanoclusters have been analyzed based on data obtained from ab initio density functional theory and quantum molecular dynamics simulations. It has been found that the Al5Au5 nanocluster possesses a hollow shaped minimum energy structure with segregated Al and Au layered domains, the former representing the electrophilic domain and the latter the nucleophilic domain. In particular, it has been shown that alkali metal cations attach in the nucleophilic domain and hop from one Au site to the next one in the picoseconds time scale, while anions are bound tightly to the Al atoms of the electrophilic domain. Simulating annealing studies are very suggestive of the proneness of the nanocluster towards coalescence into large cluster units, when the cluster is left unprotected by appropriate ligands. Further passivation studies with NaF salt suggest, nonetheless, the possibility of the isolation of the Al5Au5 cluster in molten salts or ionic liquids.